Copy number variation of genes (exons) in invasive Cottus compared to the parental species, Cottus rhenanus and Cottus perifretum.. Copy number variation of genes (exons) in invasive Cottus compared to the parental species, Cottus rhenanus and Cottus perifretum.

Hybridization between Cottus rhenanus and C. perifretum has resulted in an evolutionary young hybrid lineage of invasive Cottus that has colonized a new habitat where the parental species are not found (Nolte et al. 2005; Proc. R. Soc. B 272: 2379–2387). This CGH array was designed to screen for copy number variation among Cottus species and to find gene duplicates that are unique to the hybrid lineage (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin). Overall design: SurePrint G3 custom CGH 8x60k microarray with five technical replicates per probe and a 15 bp linker added to each probe as recommended by Agilent. The experimental design was a two-color experiment (Cottus individual vs. common reference) with 24 biological replicates (3 species x 8 individuals). Each Cottus individual was co-hybridized with the same Cottus perifretum individual as a common reference. The normalization procedure included a calibration step to account for probe-specific binding behavior, which was assessed using a custom designed calibration array (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).